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Old 11-06-2017, 01:16 AM   #1
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Location: Cambridge MA

Join Date: Oct 2017
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Default salmon tximport file vector question

Sorry for the noob question which is probably due to my poor understanding of R... Salmon generates a folder with the sample name for each sample, with inside it, a quant.sf file. Can someone give me a concrete example of how I define the files in the tximport statement. The sample code below from Mike Love doesn't help me, as it seems to have toy names.

files <- file.path(dir, "salmon", samples$run, "quant.sf")
names(files) <- paste0("sample", 1:6)
txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene, reader = read_tsv)

Thanks in advance
humphreyg is offline   Reply With Quote
Old 11-06-2017, 04:52 PM   #2
Location: MA, USA

Join Date: Feb 2014
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Hi humphreyg,

Those commands are building up a 'named vector' of the location of each file. You could manually give it the location of each file like so:

files <- c("salmon/sample1/quant.sf", "salmon/sample2/quant.sf", "salmon/sample3/quant.sf")

names(files) <- c("sample1", "sample2", "sample3")

You'll need to replace "sample1", etc., with the actual names and locations of your files.


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